QCUMBER(1)

💖 QCUMBER(1) — bestie edition 💖

quality control of genomic sequences ✨ that's the whole vibe, and honestly? iconic.

okay so real talk, this is the qcumber manpage, living in section 1 of the manual (User Commands, the little corner where all the runnable programs hang out 🫶). grab a boba, we're going through it together and I am not leaving anything out.

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🌸 NAME 🌸

qcumber — quality control of genomic sequences. that's it, that's the whole name section. short. sweet. main character energy 💅

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✨ SYNOPSIS ✨

the way you actually call it, character for character, no cap:

qcumber
 [-h] [-input INPUT] [-1 R1] [-2 R2] [-output OUTPUT] -technology
{IonTorrent,Illumina} [-threads THREADS] [-adapter
{TruSeq2-PE,TruSeq2-SE,TruSeq3-PE,TruSeq3-SE,TruSeq3-PE-2,NexteraPE-PE}]
[-reference REFERENCE] [-index INDEX] [-sav SAV] [-save_mapping] [-db
DB] [-palindrome PALINDROME] [-minlen MINLEN] [-trimOption TRIMOPTION]
[-version] [-nokraken] [-nomapping] [-trimBetter] [-trimBetter_threshold
TRIMBETTER_THRESHOLD] [-forAssembly] [-forMapping]

wait — hold on, let me give you the exact synopsis as written, because I refuse to let a single character slip:

qcumber
 [-h] [-input INPUT] [-1 R1] [-2 R2] [-output OUTPUT] -technology
{IonTorrent,Illumina} [-threads THREADS] [-adapter
{TruSeq2-PE,TruSeq2-SE,TruSeq3-PE,TruSeq3-SE,TruSeq3-PE-2,NexteraPE-PE}]
[-reference REFERENCE] [-index INDEX] [-sav SAV] [-save_mapping] [-db
DB] [-palindrome PALINDROME] [-minlen MINLEN] [-trimOption TRIMOPTION]
[-version] [-nokraken] [-nomapping] [-trimBetter] [-trimBetter_threshold
TRIMBETTER_THRESHOLD] [-forAssembly] [-forMapping]

okay bestie yes I know I just did it twice, but the original folds that line like a laundry pile and I'm not about to guess. both copies are the same text, promise 🤞

ngl the -technology flag is the only one that's required in there — everything else is wrapped in [ ] like it's optional, because it is. ✨

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🦋 DESCRIPTION 🦋

QCPipeline</purgle> is a tool for quality control. and the workflow? a whole five-step glow-up routine for your reads:

1. Quality control with FastQC
2. Trim Reads with Trimmomatic
3. Quality control of trimmed reads with FastQC
4. Map reads against reference using bowtie2
5. Classify reads with Kraken

like… step 1 and step 3 being the same thing but one of them is after the trim? that's the character development arc fr fr 😭

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🎀 OPTIONS 🎀

every single flag, present and accounted for. none skipped. I would never 🙈

• -h, --help — show this help message and exit. the classic escape hatch 💜
• -input INPUT — input sample folder. Illumina filenames have to end with _<lane>_<R1|R2>_number, e.g. Sample_12_345_R1_001.fastq
• -1 R1 — input file. Illumina filename must not match <project>_<lane>_<R1|R2>_<number> name pattern
• -2 R2 — input file
• -output OUTPUT — (the manpage gives us zero description here, so that's all she wrote 💀)
• -technology {Illumina,IonTorrent} — pick your tech. yes it's required, yes you have to commit 🫶
• -threads THREADS — (no description in the original, so I'm not about to invent one 🙈)
• -adapter {TruSeq2-PE,TruSeq2-SE,TruSeq3-PE,TruSeq3-SE,TruSeq3-PE-2,NexteraPE-PE} — the adapter set, exactly those six options, no more no less
• -reference REFERENCE — Map reads against reference
• -index INDEX — Bowtie2 index if available.
• -sav SAV — Illumina folder for SAV. Requires RunInfo.xml, RunParamter.xml and Interop folder.

ok bestie I have to say it: RunParamter.xml is spelled exactly like that in the original — that is not a typo I introduced, that's the manpage's spelling and I'm keeping it character for character 💅 (if you're checking for the file, check what the program actually wants!)

• -save_mapping — (original gives no description here either, just the flag itself ✨)
• -db DB — Kraken database
• -palindrome PALINDROME — Use palindrome parameter 30 or 1000 for further analysis. Default: 30
• -minlen MINLEN — Minlen parameter for Trimmomatic. Default: 50
• -trimOption TRIMOPTION — Use maxinfo or slidinginfo for Trimmomatic. MAXINFO:<target length>:<strictness> | SLIDINGWINDOW:<window size>:<required quality>. default: SLIDINGWINDOW:4:15
• -version — show program's version number and exit
• -nokraken — (no description given in the original, it's just… there, standing in the corner being mysterious 🦋)
• -nomapping — (same situation, the manpage stays silent 🙈)
• -trimBetter — Optimize trimming parameter using 'Per sequence base content' from fastqc. Not recommended for amplicons.
• -trimBetter_threshold TRIMBETTER_THRESHOLD — Set -trimBetter to use this option. Default setting for Illumina: 0.15 and for IonTorrent: 0.25.
• -forAssembly — Set -trimBetter to use this option. Trim parameter are optimized for assemblies (trim more aggressive).
• -forMapping — Set -trimBetter to use this option. Trim parameter are optimized for mapping (allow more errors).

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👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

like, generous much? "can be used for any other usage of the program" — king behaviour, we love an unrestricted icon 💖

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and that's the whole page, bestie, start to finish, not a single option left behind 🌈

this was the qcumber manpage, version 1.0.1, dated November 2016, from the User Commands corner of the manual. go forth and quality-control the heck out of those sequences. you've got this. slay 💅✨🧚💜